Report common T-cell receptor sequences
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
After merging the reads and checking for the V3LOOP amplicon, check for T-cell receptor alpha and beta (TCA and TCB) matches. Take all of those matches, and report the most common nucleotide sequences, by exact match. For the first version, report any sequences with prevalence of at least 5% of all T-cell receptor matches.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Trace the pipeline from read merging through the V3LOOP amplicon check, then find where TCA and TCB matches are identified and reported. Implement reporting of exact nucleotide-sequence matches whose prevalence is at least 5% of all T-cell receptor matches, and verify the output against representative FASTQ processing results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100